chr4-146866593-T-C

Position:

• chr4-146866593-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000325106.9(TTC29):​c.885+905A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.666 in 151,946 control chromosomes in the GnomAD database, including 35,918 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.67 (35918 hom., cov: 31)
• Consequence: TTC29 ENST00000325106.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88

Genes affected

TTC29 (HGNC:29936): (tetratricopeptide repeat domain 29) Involved in cilium movement and cilium organization. Located in sperm flagellum. Implicated in spermatogenic failure 42. [provided by Alliance of Genome Resources, Apr 2022]

TTC29 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.909 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TTC29	NM_031956.4	c.885+905A>G		intron_variant		ENST00000325106.9	NP_114162.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TTC29	ENST00000325106.9	c.885+905A>G		intron_variant		1	NM_031956.4	ENSP00000316740.4
TTC29	ENST00000508306.5	n.885+905A>G		intron_variant		1		ENSP00000422648.1
TTC29	ENST00000513335.5	c.963+905A>G		intron_variant		2		ENSP00000423505.1
TTC29	ENST00000504425.5	c.885+905A>G		intron_variant		5		ENSP00000425778.1

Frequencies

GnomAD3 genomes AF: 0.665 AC: 101012 AN: 151828 Hom.: 35854 Cov.: 31

Gnomad AFR AF: 0.917

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.687

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.755

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.643

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.666 AC: 101129 AN: 151946 Hom.: 35918 Cov.: 31 AF XY: 0.670 AC XY: 49752 AN XY: 74272

Gnomad4 AFR AF: 0.917

Gnomad4 AMR AF: 0.687

Gnomad4 ASJ AF: 0.595

Gnomad4 EAS AF: 0.754

Gnomad4 SAS AF: 0.664

Gnomad4 FIN AF: 0.592

Gnomad4 NFE AF: 0.517

Gnomad4 OTH AF: 0.647

Alfa AF: 0.536 Hom.: 26770

Bravo AF: 0.683

Asia WGS AF: 0.753 AC: 2618 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.032
DANN	Benign	0.45

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1396716; hg19: chr4-147787745;